The court will hear the CBI application on Wednesday.
Pandey finally surrendered in an Ahmedabad court on Tuesday.
The Supreme Court on Monday rejected his anticipatory bail plea in connection with the case.
The apex court said it rejected his bail plea since he remained an absconder in the case.
The Gujarat Police on Saturday claimed Pandey had gone missing again.
According to the police, Pandey was missing since the Gujarat High Court on Wednesday rejected his anticipatory bail plea.
Following the rejection, a Central Bureau of Investigation (CBI) court had issued a non-bailable warrant against the police officer.
Nineteen-year-old Ishrat was gunned down by the Gujarat Police along with Javed Ghulam Sheikh alias Pranesh Kumar Pillai, Amjad Ali alias Rajkumar Akbar Ali Rana and Jisan Johar Abdul Gani in Ahmedabad on June 15, 2004.
The police alleged that Ishrat and three others were Lashkar-e-Taiba (LeT) militants who conspired to assassinate Gujarat Chief Minister Narendra Modi.
--IBNS (Posted on 14-08-2013)